Re: [Anuga-user] Problem with runtests.py / _intel_fast_memset issue

[Christos A. <alt...@gm...>]

Hi Steve,

Thanks a lot for the immediate response. Thank you for the links as well as
the suggestions. I was already aware of the two first links and while I
forced loading only gcc, I still  have the same issues.

Currently I am trying to setup everything through a local conda
environment. After I complete this try, I will isolate the conda
environment and load my previous python setup in order to try what you
suggested.

I will let you know of my progress.

Notifying the admins on Friday afternoon, August 2 in Europe!! My chances
are not that high. I will let them know on Monday.

Thanks a lot again.

Best
Christos

On Fri, Aug 2, 2019 at 3:49 PM Stephen Roberts <ste...@an...>
wrote:

> Hi Christos,
>
>
> It would be interesting to see the output of
>
>
> python setup.py clean
>
> python setup.py build 2>&1 | tee build.log
>
>
> The content of build.log might give us a hint as to where the intel
> command is coming from.
>
>
> I suppose you have talked to your system admin people?
>
>
> Some interesting discussions
>
>
> https://mail.python.org/pipermail//scikit-image/2015-October/004333.html
>
>
> https://groups.google.com/forum/#!topic/scikit-image/iSgNGBG0ZqU
>
>
> and
>
>
>
> https://christoph-conrads.name/building-numpy-and-scipy-with-intel-compilers-and-intel-mkl/
>
>
> It has been a while but we have compiled anuga using the intel compilers,
> so this third link might be an option.
>
>
> Cheers
>
> Steve
>
>
> ==============================
> Stephen Roberts
> Undergraduate Convenor
> Mathematical Sciences Institute
> Room 4.74 Hanna Neumann Building #145
> The Australian National University
> Canberra, ACT 2600 AUSTRALIA
> Ph: +61 2 61254445
> CRICOS: 00120C
>
> ------------------------------
> *From:* Christos Altantzis <alt...@gm...>
> *Sent:* Friday, 2 August 2019 8:48:48 PM
> *To:* Anu...@li... <Anu...@li...>
> *Subject:* [Anuga-user] Problem with runtests.py / _intel_fast_memset
> issue
>
> Hi Group,
>
> I have been using anuga for more than a year now and I have to admit that
> the developers have done an excellent job. I really thank you for this.
> Until now I have been working on local machines and I never had a problem.
>
> Currently, I am trying ti install ANUGA on a cluster where I do not have
> superuser rights, so I am trying to install the code from source. I have
> managed to install all the dependencies and all of them seem to be working
> properly. Build_all.py works without problems and the installation seems to
> be fine. Then when I am trying to import anuga or run the runtests.py I get
> the following error:
>
> Building, see build.log...
> Build OK
> Traceback (most recent call last):
>   File "runtests.py", line 402, in <module>
>     main(argv=sys.argv[1:])
>   File "runtests.py", line 201, in main
>     __import__(PROJECT_MODULE)
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/__init__.py",
> line 69, in <module>
>     from anuga.shallow_water.shallow_water_domain import Domain
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
> line 100, in <module>
>     from anuga.abstract_2d_finite_volumes.generic_domain \
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/abstract_2d_finite_volumes/generic_domain.py",
> line 22, in <module>
>     from quantity import Quantity
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
> line 30, in <module>
>     from anuga.fit_interpolate.fit import fit_to_mesh
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/fit_interpolate/fit.py",
> line 33, in <module>
>     from anuga.fit_interpolate.general_fit_interpolate import
> FitInterpolate
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/fit_interpolate/general_fit_interpolate.py",
> line 26, in <module>
>     from anuga.utilities.sparse import Sparse, Sparse_CSR
>   File
> "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/utilities/sparse.py",
> line 335, in <module>
>     from sparse_ext import csr_mv
> ImportError:
> /cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/utilities/sparse_ext.so:
> undefined symbol: _intel_fast_memset
>
> The problem is this _intel_fast_memset. I made sure that I do not load any
> icc in my bashrc and that only gcc is used, and still I see this problem.
> Is it possible that this happens due to the fact that some of the
> dependencies might have been built with icc?? Have you encountered such an
> issue in the past?? I am struggling to resolve this issue but I am out of
> ideas.
>
> If anything else fails I will try to install locally conda and do
> everything through conda, but if somebody has some experience with a
> similar problem I would appreciate sharing his/her experience.
>
> Best
> Christos
>